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Table 3 Parameter estimates for UCP genes under different branch models, site models and branch-site models

From: Evolutionary history of the UCP gene family: gene duplication and selection

Model

Parameters for branches

Positively selected sites

Likelihood

One-Ratio

ω0 = 0.07649

None

-15704.05

Branch specific

   

Two-ratios (R2)

ω0 = 0.0950

None

-15696.32

 

ω1 = 0.0660

  

Three-ratios (R3)

ω0 = 0.0946

None

-15686.87

 

ω1 = 0.0845

  
 

ω2 = 0.0496

  

Site specific

   

Neutral (M1)

ω0 = 0.0657, ρ0 = 0.92529

Not allowed

-15586.80

 

ω1 = 1, ρ1 = 0.07471

  

Selection (M2)

ω0 = 0.06571, ρ0 = 0.9253

 

-15586.80

 

ω1 = 1, ρ1 = 0.07470

  
 

ω2 = 1.266, ρ2 = 0.00000

  

Discrete (M3)

ω0 = 0.1109, ρ0 = 0.49068

 

-15244.05

(K = 3)

ω1 = 0.10086, ρ1 = 0.38265

  
 

ω2 = 0.32064, ρ2 = 0.12668

  

Beta (M7)

ρ = 0.50769 q = 4.86274

 

-15243.99

Beta&ω (M8)

ρ0 = 0.99, p = 0.53223

224 K (P = 0.914)

-15233.43

 

q = 5.57248, ρ1 = 0.00373, ω1 = 1.69524

  

Branch-Site

   

Model A

ρ0 = 0.9155, ρ1 = 0.04732,

In the foreground lineage:

-15563.81

 

ρ2a = 0.03529, ρ2b = 0.00182

180 H (P = 0.953), 220 L (P = 0.997), 235 M (P = 0.969)

 
 

ω2 = 0.06259

  

Model B

ρ0 = 0.49203, ρ1 = 0.43366,

In foreground lineage:

-15264.48

 

ρ2a = 0.03950, ρ2b = 0.03481

No significant sites

 
 

ω0 = 0.012, ω1 = 0.12812, ω2 = 0.52

In the background lineage:

 
  

no significant site

 
  1. The models were implemented in Codeml from PAML. Parameters in bold indicate positive selection.